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Protein interface classification by evolutionary analysis
2012
BMC Bioinformatics
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In that case, no evolutionary prediction is run and interface classification relies on core size only. ...
This allows us to formulate an interface assignment even when not enough homologs to the query are available for evolutionary analysis. ...
doi:10.1186/1471-2105-13-334
pmid:23259833
pmcid:PMC3556496
fatcat:npelnu2c3vdkpio7u556itfmky
Structure, function, and evolution of transient and obligate protein-protein interactions
2005
Proceedings of the National Academy of Sciences of the United States of America
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from an evolutionary perspective. ...
We address these and other questions by relying on a carefully curated dataset of protein complex structures. ...
J.M. is supported by the Department of Energy Computational Science Graduate Fellowship͞ Krell Institute. ...
doi:10.1073/pnas.0502667102
pmid:16043700
pmcid:PMC1182425
fatcat:pmdjo4wnancjdcrxiofgzsdsvi
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures
2019
Nucleic Acids Research
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The Structural Classification of Proteins (SCOP) database is a classification of protein domains organised according to their evolutionary and structural relationships. ...
We have also improved the database schema, provided a new API and modernised the web interface. ...
The classification of proteins in SCOP has been constructed mainly manually by visual inspection and analysis. ...
doi:10.1093/nar/gkz1064
pmid:31724711
pmcid:PMC7139981
fatcat:i45ut5wpvnafnpu4mmuk4lm25m
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts
2015
Bioinformatics
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A key issue linked to protein interface classification is the identification of the biological assembly of a crystal structure and the analysis of its symmetry. ...
This review provides an overview of the concepts and main approaches to protein interface classification: thermodynamic estimation of interface stability, evolutionary approaches based on conservation ...
Interface classification and docking Protein interface classification has close ties with the field of protein-protein docking. ...
doi:10.1093/bioinformatics/btv622
pmid:26508758
pmcid:PMC4743631
fatcat:y5taf2mmlfgtxjjqjb7ghiqvxu
Structural Determinants of Protein Evolution Are Context-Sensitive at the Residue Level
2009
Molecular biology and evolution
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The relationship between solvent exposure and evolutionary rate (d N /d S ) is found to be strong, positive, and linear. ...
burial and a more surprising fixed functional constraint that accompanies any degree of interface involvement. ...
correct classification rates. ...
doi:10.1093/molbev/msp146
pmid:19597162
fatcat:iaqlhlhfafdslib7sq7h6kfxzq
Structural Mapping of Protein Interactions Reveals Differences in Evolutionary Pressures Correlated to mRNA Level and Protein Abundance
2007
Structure
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To determine how this constraint affects the evolution of protein interactions, we directly measure evolutionary rates of protein interface, surface, and core residues by structurally mapping domain interactions ...
Interfaces of proteins with low mRNA levels may have higher evolutionary flexibility and could constitute the raw material for new functions. ...
Statistical Analysis The R package was used for statistical analysis (Ihaka and Gentleman, 1996) . ...
doi:10.1016/j.str.2007.09.010
pmid:17997970
pmcid:PMC2600897
fatcat:tvg2s2ji7nexxev5prmwnt5iwy
ACLAME: A CLAssification of Mobile genetic Elements, update 2010
2009
Nucleic Acids Research
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The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added. ...
The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). ...
On the 'Classification' page, users can display the entire graph or only the most closely related MGEs by using the Cytoscape button. ...
doi:10.1093/nar/gkp938
pmid:19933762
pmcid:PMC2808911
fatcat:mb35plb5mzfvlh7hxovbd7logy
An analysis of oligomerization interfaces in transmembrane proteins
2013
BMC Structural Biology
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In our set, membrane lipids were not found to significantly mediate protein-protein interfaces. ...
The general features of TM interfaces do not differ much from those of soluble proteins: they are large, tightly packed and possess many interface core residues. ...
and evolutionary analysis. ...
doi:10.1186/1472-6807-13-21
pmid:24134166
pmcid:PMC4015793
fatcat:yijecrbw7rf4honpxpay5tdiey
Understanding protein evolutionary rate by integrating gene co-expression with protein interactions
2010
BMC Systems Biology
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Analysis of hub proteins in the Structural Interaction Network further supported ePPID as a better predictor of protein evolutionary rate than the number of distinct binding interfaces and clarified the ...
slower evolution of co-expressed multi-interface hub proteins over that of other hub proteins. ...
Acknowledgements XM is supported by NIH grant HG001696 to Michael Q Zhang. ...
doi:10.1186/1752-0509-4-179
pmid:21190591
pmcid:PMC3022652
fatcat:yoj6ite67zhvtf4lfigz76yj5a
The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry
2006
PLoS Computational Biology
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We show that any evolutionary analysis on interfaces can be skewed by multiple binding orientations and multiple interaction partners. ...
A systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. ...
Funding through the EFRE (Europä ischer Fonds fü r regionale Entwicklung) projects CODI (Classification of Domain Interfaces), FoldUnfold, GoEverywhere, and the European Union IST projects Sealife and ...
doi:10.1371/journal.pcbi.0020124
pmid:17009862
pmcid:PMC1584320
fatcat:npvjydlqa5bcjpfvfmybphjxpq
The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry
2005
PLoS Computational Biology
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We show that any evolutionary analysis on interfaces can be skewed by multiple binding orientations and multiple interaction partners. ...
A systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. ...
Funding through the EFRE (Europä ischer Fonds fü r regionale Entwicklung) projects CODI (Classification of Domain Interfaces), FoldUnfold, GoEverywhere, and the European Union IST projects Sealife and ...
doi:10.1371/journal.pcbi.0020124.eor
fatcat:cowc33cez5hgvjaxxijkvcatqu
Character and evolution of protein–protein interfaces
2005
Physical Biology
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Protein-protein interactions create the macromolecular assemblies and sequential signaling pathways essential for cell function. ...
This paper discusses methods based on multiple sequence alignments of protein homologues and phylogenetic trees. ...
As a result the analysis of entire interface is always noisy, regardless of how it is defined. ...
doi:10.1088/1478-3975/2/2/s04
pmid:16204847
fatcat:bjua3mjjr5gpbgrhzpjlapkoie
Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification
2018
BMC Bioinformatics
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By using a variety of machine learning approaches, we trained a new interface classification predictor based on contacts and interaction energetic features. ...
We implemented our classification approach into an easy-to-use and fast software, freely available to the scientific community from http://github.com/haddocking/interface-classifier . ...
Li Xue and Panagiotis Koukos for helpful discussions over data analysis. Further, the authors thank Dr. ...
doi:10.1186/s12859-018-2414-9
pmid:30497368
pmcid:PMC6266931
fatcat:77krmd67uzgn3jb2a2qa3kpgri
RIGD: A Database for Intronless Genes in the Rosaceae
2020
Frontiers in Genetics
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In addition, attribute analysis, functional annotations, subcellular localization prediction, and GO analysis are reported. The RIGD allows users to browse, search, and download data with ease. ...
Most eukaryotic genes are interrupted by one or more introns, and only prokaryotic genomes are composed of mainly single-exon genes without introns. ...
The funders had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. ...
doi:10.3389/fgene.2020.00868
pmid:32849839
pmcid:PMC7426402
fatcat:uapn3plynrcsbmvpbgtx3er5gm
Prediction of binding hot spot residues by using structural and evolutionary parameters
2009
Genetics and Molecular Biology
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In this work, we present a method for predicting hot spot residues by using a set of structural and evolutionary parameters. ...
Unlike previous studies, we use a set of parameters which do not depend on the structure of the protein in complex, so that the predictor can also be used when the interface region is unknown. ...
Structural and evolutionary parameters A set of 43 evolutionary and structural parameters, presented below, were used to characterize an interface residue. ...
doi:10.1590/s1415-47572009000300029
pmid:21637529
pmcid:PMC3036045
fatcat:udwbcpemhna5lgriayz2dcoafq
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